compile & execute a class

rapidly prototype a plugin

It is often easier to start out with a Jython, JRuby or BeanShell script, as you do not have to care about strict typing, exceptions or recompiling. Just place your script (with the correct extension -- .py, .rb or .bsh) into the plugins/ folder and execute the script. Fiji will always execute the current version of the script, so you can edit and run the script without restarting Fiji.

Once you have working code, you can turn it into a proper plugin (this is easiest with BeanShell, as its syntax is closest to Java already), adding strict typing and exception handling as needed.

find the .jar file containing a certain class

Sometimes, the compiler complains about a class not having a certain method or interface, but you know it must contain it. More often than not, that class exists in different versions in your classpath. Find out with

$ ./fiji bin/find-jar-for-class.py the.class.youre.looking.For

Using ImageJ effectively

ImageJ has a simple API, but it is also big, so here are a few pointers to some useful parts.

How to read a file into an ImagePlus

ImagePlus image = IJ.openImage(path);

How to display an exception in a window

This is especially useful on Windows, where you usually do not see the console:

IJ.handleException(exception);

This is available since ImageJ 1.43g, as well as the option to set a different exception handler using